T - Genome Annotation & Analyzing Genetic Variation

reference genomes

well-characterized standards used for bioinformatic comparisons

a reference genome is NOT

• the genome of a single individual (usually)

• synonymous with “wild type” or “normal”

• 100% perfectly assembled or complete (it may be improved over time!)

Annotating a genome involves

finding and labeling functional elements

you can know what parts of the genome correspond to

genes, promoters, enhancers, etc

bioinformatics tools and databases

allow genomes to be computationally explored and compared

long ORFs

identify candidate genes in a genome

Genome sequences are typically reported for just ___ strand, because that is enough to figure out the sequence of the ________ strand.

one, complementary 

A protein-coding sequence could be located in ____ strand, in any reading frame. We must check all ___!

either, six

If you locate a reading frame that is open for hundreds of bp, you are likely looking at part of a

protein coding sequence

Eukaryotic ORFs

may be disrupted by introns, complicating ORF prediction

Another gene prediction strategy takes advantage of

common ancestry

The more ____ two species shared a common ancestor, the more ____ their genomes will be (less time for mutations to accumulate that are the source of genetic diversity!)

recently, similar

Although new mutations can arise randomly anywhere…

…changes that affect genes are more likely to affect fitness and be eliminated by natural selection.

Genes often have ____ conservation between species

high

Transcriptomic data

can confirm whether a predicted gene is actually a functional gene

Knowing what ____ are present in a cell can help identify genes that are actively transcribed

mRNAs

mRNAs are prone to degradation, so one way to study the transcriptome of a cell is to make a ____ copy of all the mRNAs

DNA

cDNA libraries

only contain sequences found in mature mRNAs made by that cell

a cDNA library will contain 

protein coding ORFs

a cDNA library will NOT contain 

promoters or enhancers

alternative splicing 

not all exons will be present in mature mRNAs

Most of the human genome is shared, yet we still have a tremendous amount of

genetic variation

a causitive difference is obvious when there is

• Deletion or of a required enhancer

• Mutation that prevents key TFs from binding the promoter

• deletion of coding region, early nonsense coding mutation

SNPs

single-nucleotide differences between genomes

linked SNPs

no effect on protein production or function 

causative SNPs

noncoding SNP or coding SNP

noncoding SNP

changes amount of protein produced

coding SNP

changes amino acid sequence

A SNP will initially be found in only ___ combination with all the other SNPs on the ___ chromosome

one, same

SNPs on a chromosome will be inherited as a unit unless they are separated by

recombination

Recombination rates are not _____ across the genome

uniform

Some regions of the genome have such a low rates of recombination that all nucleotides in that region are _______ _____ to each other

completely linked

People with the same haplotype

share all the same completely linked SNPs in that particular region

A few ____ SNPs can be used to group people who share MANY SNPs within a haplotype block

marker

SNPs that do not _____ a mutant phenotype may still be useful as linked markers

cause

Sequencing marker SNPs can help predict some phenotypes, even if marker SNPs aren’t causative…

…and even if we don’t know what actually is causative

We often do not know what causes certain traits since

In many cases, it may involve the effects of multiple genes, which complicates things further

SNP analysis relies on

sequencing

A SNP does not change the ____ of DNA, so PCR + gel electrophoresis will ___ distinguish between SNPs

size, not

things that change the number of bases in a region

Single sequence repeats (SSRs), indels, and copy number variants

DNA fingerprinting relies on highly variable

SSR loci

Primers are designed that amplify the ___ region— alleles with more repeats

make ____ PCR products

entire, bigger

DNA fingerprinting looks at the sizes of PCR products made from

all 20 loci